Review on the QM/MM Methodologies and Their Application to Metalloproteins
The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-04-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/27/9/2660 |
| _version_ | 1797503836607217664 |
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| author | Christina Eleftheria Tzeliou Markella Aliki Mermigki Demeter Tzeli |
| author_facet | Christina Eleftheria Tzeliou Markella Aliki Mermigki Demeter Tzeli |
| author_sort | Christina Eleftheria Tzeliou |
| collection | DOAJ |
| description | The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor. |
| first_indexed | 2024-03-10T03:56:03Z |
| format | Article |
| id | doaj.art-e3e0c11513004926869faed043fb6414 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T03:56:03Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-e3e0c11513004926869faed043fb64142023-11-23T08:47:44ZengMDPI AGMolecules1420-30492022-04-01279266010.3390/molecules27092660Review on the QM/MM Methodologies and Their Application to MetalloproteinsChristina Eleftheria Tzeliou0Markella Aliki Mermigki1Demeter Tzeli2Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, GreeceLaboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, GreeceLaboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, GreeceThe multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.https://www.mdpi.com/1420-3049/27/9/2660multiscale calculationsQM/MMDFTsemi-empiricalmolecular dynamicsmolecular mechanics |
| spellingShingle | Christina Eleftheria Tzeliou Markella Aliki Mermigki Demeter Tzeli Review on the QM/MM Methodologies and Their Application to Metalloproteins Molecules multiscale calculations QM/MM DFT semi-empirical molecular dynamics molecular mechanics |
| title | Review on the QM/MM Methodologies and Their Application to Metalloproteins |
| title_full | Review on the QM/MM Methodologies and Their Application to Metalloproteins |
| title_fullStr | Review on the QM/MM Methodologies and Their Application to Metalloproteins |
| title_full_unstemmed | Review on the QM/MM Methodologies and Their Application to Metalloproteins |
| title_short | Review on the QM/MM Methodologies and Their Application to Metalloproteins |
| title_sort | review on the qm mm methodologies and their application to metalloproteins |
| topic | multiscale calculations QM/MM DFT semi-empirical molecular dynamics molecular mechanics |
| url | https://www.mdpi.com/1420-3049/27/9/2660 |
| work_keys_str_mv | AT christinaeleftheriatzeliou reviewontheqmmmmethodologiesandtheirapplicationtometalloproteins AT markellaalikimermigki reviewontheqmmmmethodologiesandtheirapplicationtometalloproteins AT demetertzeli reviewontheqmmmmethodologiesandtheirapplicationtometalloproteins |